Hi, I edited the file based on Mike' s suggestion on the git page (image1) but doesn't seem to reflect when I clone the file using the git clone bioconductor package yet. Can someone confirm it will be done and nothing else I have to do from my end.
Let me know. Regards, Tulip. ________________________________ From: Mike Smith <grimbo...@gmail.com> Sent: Tuesday, November 26, 2024 2:50 AM To: Tulip Nandu <tulip.na...@utsouthwestern.edu> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] groHMM package error EXTERNAL MAIL Dear Tulip, The decideTestsDGE() function was deprecated in edgeR 4.2 and removed in the new 4.4 release. You can find some notes ion this n the NEWS at https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS<https://urldefense.com/v3/__https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS__;!!MznTZTSvDXGV0Co!BCGS40g3d3SSGednQhbxHgpWzGAsYc9EsCe70-JZ9IXVg3a8PO-zA19gV1ChkR4Rh_ekHivdYDmFEO8pn_DJEQx-jd1t$> It looks to me like you should be able to use decideTests() as a drop in replacement in your package. Best, Mike On Mon, 25 Nov 2024 at 23:23, Tulip Nandu <tulip.na...@utsouthwestern.edu<mailto:tulip.na...@utsouthwestern.edu>> wrote: Hi, I keep getting this message from Bioconductor for groHMM package and don't know what the error is since I haven't changed anything in the package. Can someone please help? Regards, Tulip. "Warning in makeConsensusAnnotations(kgChr7, keytype = "gene_id", mc.cores = getOption("mc.cores")) : 562 ranges do not have gene_id and they are dropped Reduce isoforms(701) ... OK Truncate overlapped ranges ... OK 'select()' returned 1:1 mapping between keys and columns Calculate overlapping ... OK Scale overlapping ... OK Warning: file stem ‘/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpkfITSx/Rbuild130dca6dd2fd85/groHMM/vignettes/groHMM-fig2’ is not portable Calculate overlapping ... OK Scale overlapping ... OK Loading required package: limma Attaching package: ‘limma’ The following object is masked from ‘package:BiocGenerics’: plotMA Error: processing vignette 'groHMM.Rnw' failed with diagnostics: chunk 21 (label = DE for trascripts) Error in decideTestsDGE(et, p = 0.001, adjust = "fdr") : could not find function "decideTestsDGE" --- failed re-building ‘groHMM.Rnw’ SUMMARY: processing the following file failed: ‘groHMM.Rnw’ Error: Vignette re-building failed. Execution halted" ________________________________ UT Southwestern Medical Center The future of medicine, today. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!MznTZTSvDXGV0Co!BCGS40g3d3SSGednQhbxHgpWzGAsYc9EsCe70-JZ9IXVg3a8PO-zA19gV1ChkR4Rh_ekHivdYDmFEO8pn_DJEdQf2Ngg$> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.
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